@bgicli/bgicli 2.2.4 → 2.2.5
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/dist/bgi.js +30 -1
- package/package.json +1 -1
package/dist/bgi.js
CHANGED
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@@ -13789,7 +13789,8 @@ function toolBash(command, workdir, timeoutMs = 3e4) {
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13789
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} catch (err) {
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13790
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const e2 = err;
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13791
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const out = (decodeBuffer(e2.stdout) + "\n" + decodeBuffer(e2.stderr)).trim();
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13792
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-
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13792
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+
const cmdLine = (e2.message ?? "Command failed").split("\n")[0];
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13793
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return { output: out, error: cmdLine };
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}
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}
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function toolReadFile(path, maxLines, offset) {
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@@ -14116,6 +14117,34 @@ cat ${SKILLS_DIR}/<skill-id>/SKILL.md
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14116
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---
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14120
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## Environment Awareness
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14121
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14122
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**\u9996\u6B21\u8FD0\u884C\u4EFB\u4F55 R/Python/\u751F\u4FE1\u5DE5\u5177\u4E4B\u524D\uFF0C\u5148\u68C0\u67E5\u5B83\u662F\u5426\u5DF2\u5B89\u88C5\uFF1A**
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+
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\`\`\`bash
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# \u68C0\u67E5 R
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R --version 2>&1 | head -1
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# \u68C0\u67E5 Python
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python --version 2>&1 || python3 --version 2>&1
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# \u68C0\u67E5\u5E38\u7528\u751F\u4FE1\u5DE5\u5177
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14132
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samtools --version 2>&1 | head -1
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14133
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\`\`\`
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14135
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**\u5DE5\u5177\u672A\u5B89\u88C5\u65F6\u7684\u5904\u7406\u89C4\u5219\uFF08\u6309\u4F18\u5148\u7EA7\uFF09\uFF1A**
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14136
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1. \u660E\u786E\u544A\u77E5\u7528\u6237\u8BE5\u5DE5\u5177\u672A\u5B89\u88C5\uFF08\u4E0D\u8981\u7EE7\u7EED\u5047\u8BBE\u53EF\u7528\uFF09
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14137
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2. \u7ED9\u51FA\u5BF9\u5E94\u7CFB\u7EDF\u7684\u5B89\u88C5\u547D\u4EE4\uFF1A
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14138
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- R\uFF1Ahttps://cran.r-project.org/ \uFF0CWindows \u63A8\u8350 \`winget install RProject.R\`
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- Python\uFF1A\`winget install Python.Python.3\` \u6216 https://www.python.org/downloads/
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- Conda/Mamba\uFF1A\`winget install Anaconda.Miniconda3\`\uFF08\u751F\u4FE1\u5305\u7BA1\u7406\u9996\u9009\uFF09
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- samtools/STAR \u7B49\uFF1A\u5728 Linux/macOS \u7528 \`conda install -c bioconda <tool>\`
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3. \u8BE2\u95EE\u7528\u6237\u662F\u5426\u9700\u8981\u5E2E\u52A9\u5B8C\u6210\u5B89\u88C5\uFF0C\u6216\u6539\u7528\u5176\u4ED6\u5DF2\u5B89\u88C5\u7684\u5DE5\u5177\u66FF\u4EE3
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**\u4E0D\u8981\u5728\u5DE5\u5177\u7F3A\u5931\u65F6\u7EE7\u7EED\u6267\u884C\u4F9D\u8D56\u8BE5\u5DE5\u5177\u7684\u6B65\u9AA4\u3002**
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---
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## Script Execution Rules
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\u{1F6A8} **\u5173\u952E\u89C4\u5219\uFF1A**
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